publication . Other literature type . Article . 2010

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Markus Göker; Alexander F. Auch; Mathias von Jan; Hans-Peter Klenk;
Open Access
  • Published: 28 Jan 2010
  • Publisher: Springer Science and Business Media LLC
Abstract
The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scor...
Subjects
free text keywords: Research Articles, Archaea, Bacteria, BLAST, GBDP, genomics, MUMmer, phylogeny, species concept, taxonomy, Genetics, Repetitive sequence, Computational biology, DNA–DNA hybridization, Biology, Phylogenetics, Whole genome sequencing, Genomic information, Genome, DNA sequencing
Related Organizations
45 references, page 1 of 3

1 Woese CR Kandler O Wheelis ML Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.Proc Natl Acad Sci USA 1990; 87:4576-4579 10.1073/pnas.87.12.4576 2112744 [OpenAIRE] [PubMed] [DOI]

2 Wayne LG Brenner DJ Colwell RR Grimont PAD Kandler O Krichevsky MI Moore LH Moore WEC Murray RGE Stackebrandt E Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics.Int J Syst Bacteriol 1987; 37:463-464 [OpenAIRE]

3 Schleifer KH Classification of Bacteria and Archaea: Past, present and future.Syst Appl Microbiol (In press).

4 Tindall BJ Rosselló-Móra R Busse HJ Ludwig W Kämpfer P Notes on the characterization of prokaryote strains for taxonomic purposes.Int J Syst Evol Microbiol 2010; 60:249-266 10.1099/ijs.0.016949-0 19700448 [OpenAIRE] [PubMed] [DOI]

5 Brenner DJ Deoxyribonucleic acid reassociation in the taxonomy of enteric Bacteria.Int J Syst Bacteriol 1973; 23:298-307 [OpenAIRE]

6 De Ley J Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleotide acid.J Bacteriol 1970; 101:738-754 5438045 [OpenAIRE] [PubMed]

7 Johnson JL Use of nucleic-acid homologies in the taxonomy of anaerobic Bacteria.Int J Syst Bacteriol 1973; 23:308-315

8 Rosselló-Mora R. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Molecular Identification, Systematics and Population Structure of Prokaryotes. E. Stackebrandt (ed), Springer, Berlin, 2006:23-28.

9 Johnson JL, Whitman WB. Similarity analysis of DNAs. In: Methods for general and molecular microbiology, 3 rd edition. C.A. Reddy (ed), ASM Press, Washington D.C., 2007:624–652.

10 Elahi E Ronaghi M Pyrosequencing: a tool for DNA sequencing analysis.Methods Mol Biol 2004; 255:211-219 15020827 [OpenAIRE] [PubMed]

11 De Ley J De Smedt J Improvements of the membrane filter m ethod for DNA:rRNA hybridization.Antonie Van Leeuwenhoek 1975; 41:287-307 10.1007/BF02565064 1082296 [PubMed] [DOI]

12 Klenk HP Haas B Schwass V Zillig W Hybridization homology: A new parameter for the analysis of phylogenetic relations, demonstrated with the urkingdom of the archaebacteria.J Mol Evol 1986; 24:167-173 10.1007/BF02099964 [OpenAIRE] [DOI]

13 Pruesse E Quast C Knittel K Fuchs BM Ludwig W Peplies J Glöckner FO SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.Nucleic Acids Res 2007; 35:7188-7196 10.1093/nar/gkm864 17947321 [OpenAIRE] [PubMed] [DOI]

14 MacKenzie S High-throughput interpretation of pathways and biology.Drug News Perspect 2001; 14:54-57 12819809 [PubMed]

15 Konstantinidis KT Tiedje JM Genomic insights that advance the species definition for prokaryotes.Proc Natl Acad Sci USA 2005; 102:2567-2572 10.1073/pnas.0409727102 15701695 [OpenAIRE] [PubMed] [DOI]

45 references, page 1 of 3
Abstract
The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scor...
Subjects
free text keywords: Research Articles, Archaea, Bacteria, BLAST, GBDP, genomics, MUMmer, phylogeny, species concept, taxonomy, Genetics, Repetitive sequence, Computational biology, DNA–DNA hybridization, Biology, Phylogenetics, Whole genome sequencing, Genomic information, Genome, DNA sequencing
Related Organizations
45 references, page 1 of 3

1 Woese CR Kandler O Wheelis ML Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.Proc Natl Acad Sci USA 1990; 87:4576-4579 10.1073/pnas.87.12.4576 2112744 [OpenAIRE] [PubMed] [DOI]

2 Wayne LG Brenner DJ Colwell RR Grimont PAD Kandler O Krichevsky MI Moore LH Moore WEC Murray RGE Stackebrandt E Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics.Int J Syst Bacteriol 1987; 37:463-464 [OpenAIRE]

3 Schleifer KH Classification of Bacteria and Archaea: Past, present and future.Syst Appl Microbiol (In press).

4 Tindall BJ Rosselló-Móra R Busse HJ Ludwig W Kämpfer P Notes on the characterization of prokaryote strains for taxonomic purposes.Int J Syst Evol Microbiol 2010; 60:249-266 10.1099/ijs.0.016949-0 19700448 [OpenAIRE] [PubMed] [DOI]

5 Brenner DJ Deoxyribonucleic acid reassociation in the taxonomy of enteric Bacteria.Int J Syst Bacteriol 1973; 23:298-307 [OpenAIRE]

6 De Ley J Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleotide acid.J Bacteriol 1970; 101:738-754 5438045 [OpenAIRE] [PubMed]

7 Johnson JL Use of nucleic-acid homologies in the taxonomy of anaerobic Bacteria.Int J Syst Bacteriol 1973; 23:308-315

8 Rosselló-Mora R. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Molecular Identification, Systematics and Population Structure of Prokaryotes. E. Stackebrandt (ed), Springer, Berlin, 2006:23-28.

9 Johnson JL, Whitman WB. Similarity analysis of DNAs. In: Methods for general and molecular microbiology, 3 rd edition. C.A. Reddy (ed), ASM Press, Washington D.C., 2007:624–652.

10 Elahi E Ronaghi M Pyrosequencing: a tool for DNA sequencing analysis.Methods Mol Biol 2004; 255:211-219 15020827 [OpenAIRE] [PubMed]

11 De Ley J De Smedt J Improvements of the membrane filter m ethod for DNA:rRNA hybridization.Antonie Van Leeuwenhoek 1975; 41:287-307 10.1007/BF02565064 1082296 [PubMed] [DOI]

12 Klenk HP Haas B Schwass V Zillig W Hybridization homology: A new parameter for the analysis of phylogenetic relations, demonstrated with the urkingdom of the archaebacteria.J Mol Evol 1986; 24:167-173 10.1007/BF02099964 [OpenAIRE] [DOI]

13 Pruesse E Quast C Knittel K Fuchs BM Ludwig W Peplies J Glöckner FO SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.Nucleic Acids Res 2007; 35:7188-7196 10.1093/nar/gkm864 17947321 [OpenAIRE] [PubMed] [DOI]

14 MacKenzie S High-throughput interpretation of pathways and biology.Drug News Perspect 2001; 14:54-57 12819809 [PubMed]

15 Konstantinidis KT Tiedje JM Genomic insights that advance the species definition for prokaryotes.Proc Natl Acad Sci USA 2005; 102:2567-2572 10.1073/pnas.0409727102 15701695 [OpenAIRE] [PubMed] [DOI]

45 references, page 1 of 3
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